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A freighter docks at Deep Space 9 so that one of its passengers may receive treatment for a condition called Kalla-Nohra. Dr. Bashir is unfamiliar with the condition, but Major Kira recognizes it and informs Commander Benjamin Sisko that Kalla-Nohra was only contracted during a mining accident at a brutal labor camp called Gallitep. As Kira helped liberate the camp at the end of the Cardassian occupation of Bajor, she asks to greet the passenger.

Arriving in the Infirmary, Kira discovers that Bashir's new patient is a Cardassian. She has the man arrested as a war criminal only to find his name, Aamin Marritza, is not listed for any crimes. Sisko sees no option but to let Marritza go, yet Kira is adamant— Marritza is a Cardassian who was present at Gallitep, which is reason enough. Sisko decides to investigate further and has the man held in custody.

Further suspicions arise when Marritza claims he has never been to Bajor, an obvious lie as Bashir's tests confirm that the man has Kalla-Nohra. Citing a conflict of interest, Sisko asks Kira to remove herself from the case, but her emotional plea and a promise that she will remain professional convince him to let her continue. When she interrogates Marritza, he claims that while he served at Gallitep, he was only a file clerk. He claims the atrocities the Bajorans believe occurred at Gallitep were an illusion meant to keep other Bajorans fearful of the Cardassians.

An investigation corroborates Marritza's story, forcing Kira to cope with the possibility he may go free. Dax offers Kira advice and a sympathetic ear, but cautions that if Marritza is wrongfully punished, then the exercise will have been pointless. A photograph from Gallitep reveals that the man being held is not Aamin Marritza but Gul Darhe'el, the "Butcher of Gallitep" who reportedly murdered thousands of Bajorans. When confronted with this information; the prisoner proudly admits to being Darhe'el. Kira is shaken.

Darhe'el seems convincing, however he lets slip the name of Kira's resistance cell during the occupation— information too obscure for him to know. Other inconsistencies in his story also stand out. Gul Dukat asserts that Darhe'el is dead (buried under one of the largest military monuments on Cardassia, where half of the population viewed his body in state, including Dukat himself); furthermore, Darhe'el was off-world during the Kalla-Nohra outbreak and thus could not possibly have the disease. Odo asks Dr. Bashir to examine the prisoner's medical history. Kira is dismissive of this and asserts that the prisoner will stand trial. Dr. Bashir learns that "Darhe'el" has undergone cosmetic surgery, leading Kira to realize that the prisoner is Marritza, as she initially believed, but he wanted to be recognized as Darhe'el.

Kira confronts the prisoner with this information. Marritza breaks down as he speaks, branding himself a coward. He begs Kira to prosecute him, insisting that Cardassia must be forced to admit its wrongdoings and that he is as guilty for remaining silent as Darhe'el was for committing the atrocities. Hence his impersonation of Darhe'el: he wanted Bajor to give him the trial and sentence that Darhe'el deserved. Kira releases him, realizing he is a good man so traumatized and remorseful from his experiences that he would give up his life to make amends. She insists that another murder is not the answer and that too many good people have already died; she will not kill another. Kira and Odo escort Marritza to a ship departing from the station. Marritza laments that now that his identity has been exposed he cannot bring about change for his people. Kira assures him that his actions were honourable; if his people are going to change, people like him are needed to lead the way. On the way out of the Promenade, Marritza is suddenly stabbed and killed by a Bajoran. When Kira demands to know why, the Bajoran echoes her earlier sentiment: being a Cardassian is reason enough. "No!", Kira realizes, "It's not".

The producers of Star Trek: Voyager attempted to re-create the critical success of "Duet" with their first-season episode "Jetrel". According to DVD commentary accompanying Voyager's second season, "Jetrel" was a conscious effort to use a similar delivery to create a metaphor for the aftermath of the atomic bombings of Hiroshima and Nagasaki. In that episode, the character Neelix is forced to confront the scientist who developed a weapon which eradicated thousands of his people.

Despite being a bottle episode, "Duet" was featured in Museum of Television and Radio's 1994 "Tribute to Excellence"[2] and became a fan favourite, described by Startrek.com as "one of DS9s — possibly even one of Treks — finest [hours]".[4] It was included in several editors' choices for a feature there entitled "You're Stranded on a Desert Asteroid ... Our Best of the Best Episodes", described by editor Sandy Stone as "when I knew DS9 really had something going on".[5] The episode "is all substance, completely engrossing in its conveyance, and it also features a tragic ending" according to Jammer's Reviews, an independent science fiction portal.[6] "I'm not sure I can write a coherent analysis of this episode," Michelle Erica Green of the popular fan site The Trek Nation began her review in 2004. "I cried just thinking about it for two days after I saw it, and I still cry when I try to discuss it."[1] It has nonetheless been noted by some fans that certain parts of the exposition appear rushed, while the believability of Marritza's death scene has been questioned.[7] This can be attributed to the need to contain the episode, as the episode is "hardly [a] story worthy of a multi-episode arc".[8]

Cast and crew responded positively to the episode as well. In the Star Trek: Deep Space Nine Companion, Armin Shimerman (Quark) observed that the episode works because of "the writing and the directing and the acting all coalescing perfectly", which Nana Visitor (Kira) believed was because it had "such important things to say".[9] Notable staff to list it among their favorites are Behr,[10]Next Generation producer Dave Rossi[11] and Companion author Terry J. Erdmann.[9]